I have a 2004 MSM. It has about 150,000 miles. I am the 3rd "adult" owner so its never been modified or wrecked.
I switched the 17" Racing Hart wheels to 15 x 8" based upon advice from Keith Tanner when I first bought it. This was an excellent upgrade - lighter wheels, better handling and a better ride. The 4.1 rear end gear is kind of too low, torsen is appreciated. 1st gear is useless basically and its over 4000 rpm in 6 gear at 80.
It looks like the turbo seals are leaking a little. An oil film in the downstream piping. This is repairable, seal kits are available, though removing the turbo is a major pain because of the way its attached. I'm told its better to just remove the entire exhaust manifold first and then deal with the turbo.
Little parts like sensors are breaking. My worry is there are some parts that were unique to the MSM that Mazda will no longer supply.
For example I am chasing down a P2006 code, meaning the manifold butterfly valves are stuck open or closed. This is the VTCS system. The car bogged way more than the usual MSM bog and the CEL came on. That was the code I got on my reader.
Its either leaky vacuum hoses, a bad sensor or the actuator for rotating the butterfly valves shaft. If its the actuator I am hosed because it a discontinued part. I changed the sensor and am getting ready to change all the vacuum hoses. Same for the actuator for the turbo relief gate. Discontinued.
Also I am changing the 4 small water hoses that go through the throttle body and oil cooler while I'm doing this. Also changing the "O" ring in the oil cooler while I'm there anyway. This requires removing the manifold brace and the alternator for access to the connections. Also I have a valve cover gasket leak, (I hope that is all it is). This is the weekend coming up I do all the work since the wife and kids took off on vacation.
Look at the radiator. If its shows any sign of yellowing, browning, or cracking its time for a change. The stock one is really good. Many aftermarket radiators do not provide enough cooling though I believe FM's cross flow is one of the good ones for the MSM.
When I had to change out the turbo's water supply hose I found the same problem, part no longer available. After lots of research I found that the hose for a CX-7 turbo would fit with minor cutting of length.
It seems like a lot of the MSM guys on the Miata forum don't know much about cars and ask beginner questions so its hard to find out workarounds for discontinued parts with out a lot of research. I've gotten better advice here from Keith and others. Its appreciated.